All:
I just wanted to follow up on my initial question about CUDA compatibility. Is it the case that AMBER does not yet work with the latest CUDA drivers? While I can still use the serial version, one of my main goals is to leverage the GPUs I have available, so I'd greatly appreciate any information about compatibility from the developers. Thanks!
Ram
On Feb 24, 2012, at 11:16 AM, Scott Le Grand wrote:
> CUDA 4.1 and AMBER should be compatible, but there's a 10% slowdown
> currently with it due to a bug in nvcc.
>
> Stick to 4.0 if you can for now...
>
>
> On Fri, Feb 24, 2012 at 8:36 AM, Mettu, Ramgopal <rmettu.tulane.edu> wrote:
>
>> To be on the safe side, I downloaded Amber and AmberTools again and
>> rebuilt everything, incorporating all bug fixes, as noted below. I get the
>> same errors as I had mentioned initially - can the developers comment on
>> CUDA 4.1 compatibility? Best,
>>
>> Ram
>>
>> On Feb 24, 2012, at 8:24 AM, Ismail, Mohd F. wrote:
>>
>>> I don't think CUDA 4.1 is supported yet.
>>>
>>>
>>> *******************************
>>> Mohd Farid Ismail
>>> Graduate Student
>>> Dept. of Chemistry/Biochemistry
>>> University of Oklahoma
>>> Norman 73019
>>>
>>> ________________________________________
>>> From: Mettu, Ramgopal [rmettu.tulane.edu]
>>> Sent: Thursday, February 23, 2012 10:45 PM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] CUDA version for Amber 11?
>>>
>>> Hi Ross,
>>> Yes, I forgot to mention that I applied all the bug fixes you mention
>> below -- any thoughts on what's happening?
>>>
>>> On Feb 23, 2012, at 10:37 PM, Ross Walker wrote:
>>>
>>>> Hi Ram,
>>>>
>>>>> As for the bug fixes, I decided to start from scratch and install a
>>>>> fresh copy of AmberTools and Amber. I was able again to correctly
>>>>> install the serial and parallel versions without errors (except for a
>>>>> few discrepancies in the test scripts). Unfortunately I get a new set
>>>>> of errors when trying to compile the CUDA binaries, that look like
>>>>> this:
>>>>
>>>> But did you take that fresh copy and apply all the bugfixes for AMBER
>> and
>>>> AMBERTools from the website? - The bugfixes are required for
>> compatibility
>>>> beyond cuda 3.2. The procedure is:
>>>>
>>>> 1) tar xvjf Amber11.tar.bz2
>>>> 2) tar xvjf AmberTools-1.5.tar.bz2
>>>> 3) export AMBERHOME=/path_to/amber11
>>>> 4) cd $AMBERHOME
>>>> 5) wget http://ambermd.org/bugfixes/AmberTools/1.5/bugfix.all
>>>> 6) patch -p0 < bugfix.all
>>>> 7) rm -f bugfix.all
>>>> 8) wget http://ambermd.org/bugfixes/11.0/bugfix.all.tar.bz2
>>>> 9) wget http://ambermd.org/bugfixes/11.0/apply_bugfix.x
>>>> 10) chmod 700 apply_bugfix.x
>>>> 11) ./apply_bugfix.x $AMBERHOME/bugfix.all
>>>> 12) cd $AMBERHOME/AmberTools/src/
>>>> 13) ./configure gnu
>>>> 14) make
>>>> 15) cd ../../
>>>> 16) cd src
>>>> 17) make serial
>>>>
>>>> At this point you have the serial (non-GPU) versions of AMBERTools and
>> AMBER
>>>>
>>>> built. Best to test them at this point.
>>>>
>>>> 18) cd $AMBERHOME/AmberTools/test/
>>>> 19) make test
>>>>
>>>> Check the test logs to see if everything worked.
>>>>
>>>> 20) cd $AMBERHOME/test
>>>> 21) make test
>>>>
>>>> Again check the test logs to see if everything worked.
>>>>
>>>> Now we can build the serial GPU code.
>>>>
>>>> 22) cd $AMBERHOME/src/
>>>> 23) make clean
>>>> 24) cd $AMBERHOME/AmberTools/src/
>>>> 25) make clean
>>>> 26) ./configure -cuda gnu
>>>> 27) cd ../../
>>>> 28) cd src
>>>> 29) make cuda
>>>>
>>>> Hopefully this time it should build correctly.
>>>>
>>>> 30) cd ../test
>>>> 31) make test.cuda
>>>>
>>>> All the best
>>>> Ross
>>>>
>>>> /\
>>>> \/
>>>> |\oss Walker
>>>>
>>>> ---------------------------------------------------------
>>>> | Assistant Research Professor |
>>>> | San Diego Supercomputer Center |
>>>> | Adjunct Assistant Professor |
>>>> | Dept. of Chemistry and Biochemistry |
>>>> | University of California San Diego |
>>>> | NVIDIA Fellow |
>>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>>>> ---------------------------------------------------------
>>>>
>>>> Note: Electronic Mail is not secure, has no guarantee of delivery, may
>> not
>>>> be read every day, and should not be used for urgent or sensitive
>> issues.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 27 2012 - 08:00:02 PST
